First - I should point out that this required almost no coding -- we already had minimization and bindings; this just added a couple of new options and a bit of stitching. I'm not sure "set picking dragMinimize" is quite the right way to do this, but it's OK for this week.
Ah, yes, what to do with it?? My organic class and I were reviewing for the final last night. I popped up methylcyclohexane and started quizzing them in relation to gauche interactions and conformations. It was quite fun to just tug on the molecule to switch from equatorial to axial or from chair to twist-boat. I think the energies in UFF might be meaningless, but the ease of manipulating the model this way was great fun and way faster than anything else I've ever used -- no setup, no special page, just pull in the molecule and start tugging. It would have been especially nice to just be able to hover over an atom or bond and delete it or modify it. I have a hunch that if you added to this a simple model building kit (mostly just a few context-sensitive drop-down menus that would appear when you hover over an atom, I think), it would pretty much take care of anything I would need in teaching about structure in relation to conformations of cyclohexane -- except for a couple of pages like http://chemapps.stolaf.edu/jmol/docs/examples-11/jmol-flot-energy.htm, which is based on a more refined optimization. (Note that you can just drag-and-drop a Spartan file from your hard drive in there, and it will display its full energy profile.) In addition, since now we can test for matches to specific conformations, already it would be simple enough to write a blank-slate page that would ask the student questions like, "Shown below is 2-methylcyclohexane. By pulling on atoms, change this model to one that is a chair conformation that has an axial methyl group." -- and then test for that using the COMPARE function. I think it opens up some interesting possibilities that we haven't had before. I was thinking before that it has "questionable pedagogic value" because obviously you can't really do this sort of thing with a molecule, but as I think about it more, you can't just click on an atom in a real molecule and invert stereochemistry at that center, either! So every "model kit" has its deceit. One wonders, though, to a certain extent, does a molecule "respond" to at least minor distortions this way? I was intrigued by how the whole molecule responded when I yanked hard on an H atom. I honestly had never thought of that before, and only had thought of interactions such as that as being far more localized. But as I play with it and think about the forces involved, I have to say I think there's something there. Still pondering this. Bob -- Robert M. Hanson Professor of Chemistry St. Olaf College 1520 St. Olaf Ave. Northfield, MN 55057 http://www.stolaf.edu/people/hansonr phone: 507-786-3107 If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
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